The present invention relates generally to a method of filling the air electrode of a molten carbonate fuel cell with electrolytes and, more particularly, to a method of manufacturing the electrolyte-filled air electrode of a molten carbonate fuel cell, which calculates the entire amount of electrolyte required for a unit cell of a fuel cell stack and fills an air electrode with electrolytes in advance without using existing electrolyte plates, so as to prevent variation in the height of the fuel cell stack attributable to the melting of the electrolyte plates and achieve uniform surface pressure balance in preprocessing for the fuel cell stack, in which the unit cells of the molten carbonate fuel cell are stacked one on top of another.